In this study, tissue isolation method, Koch’s rule, combined morphology and fungal rDNA-ITS sequence analysis method were used to isolate and identify the main pathogens causing Zanthoxylum bungeanum root rot in Gansu Longnan. At the same time, the mycelium growth rate method was used to determine the effect of different light, pH, temperature, medium, carbon source and nitrogen source on the growth of pathogenic bacteria, providing a theoretical basis for the diagnosis and control of later diseases. The results show that the main pathogen causing the root rot of Longnan Zanthoxylum bungeanum is Fusarium solani. There is no obvious difference in the growth of the colony under the light condition. The pH value of suitable colony growth is 5-7, the optimum temperature is 25-30℃, the optimum medium is PDA, glucose and lactose are the best carbon source, and sodium nitrate is the best nitrogen source. Therefore, the main pathogens and the biological characteristics of the pathogens of Longnan Zanthoxylum bungeanum root rot are clarified, which provides a theoretical basis for the later study of the pathogenic mechanism and comprehensive control of the root rot of Zanthoxylum bungeanum.